119 lines
2.7 KiB
Go
119 lines
2.7 KiB
Go
package wfa
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type Result struct {
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Score int
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CIGAR string
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}
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type Penalty struct {
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M int
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X int
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O int
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E int
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}
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type traceback byte
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const (
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OpenIns traceback = iota
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ExtdIns
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OpenDel
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ExtdDel
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Sub
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Ins
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Del
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End
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)
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type WavefrontComponent struct {
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lo *PositiveSlice[int] // lo for each wavefront
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hi *PositiveSlice[int] // hi for each wavefront
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W *PositiveSlice[*Wavefront[int]] // wavefront diag distance for each wavefront
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A *PositiveSlice[*Wavefront[traceback]] // compact CIGAR for backtrace for each wavefront
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}
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func NewWavefrontComponent(preallocateSize int) WavefrontComponent {
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// new wavefront component = {
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// lo = [0]
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// hi = [0]
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// W = []
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// A = []
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// }
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w := WavefrontComponent{
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lo: &PositiveSlice[int]{
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data: []int{0},
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valid: []bool{true},
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},
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hi: &PositiveSlice[int]{
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data: []int{0},
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valid: []bool{true},
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},
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W: &PositiveSlice[*Wavefront[int]]{
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defaultValue: &Wavefront[int]{
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data: []int{0},
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valid: []bool{false},
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},
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},
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A: &PositiveSlice[*Wavefront[traceback]]{
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defaultValue: &Wavefront[traceback]{
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data: []traceback{0},
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valid: []bool{false},
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},
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},
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}
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w.lo.Preallocate(preallocateSize)
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w.hi.Preallocate(preallocateSize)
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w.W.Preallocate(preallocateSize)
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w.A.Preallocate(preallocateSize)
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return w
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}
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// get value for wavefront=score, diag=k => returns ok, value
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func (w *WavefrontComponent) GetVal(score int, k int) (bool, int) {
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return w.W.Valid(score) && w.W.Get(score).Valid(k), w.W.Get(score).Get(k)
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}
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// set value for wavefront=score, diag=k
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func (w *WavefrontComponent) SetVal(score int, k int, val int) {
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w.W.Get(score).Set(k, val)
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}
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// get alignment traceback for wavefront=score, diag=k => returns ok, value
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func (w *WavefrontComponent) GetTraceback(score int, k int) (bool, traceback) {
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return w.A.Valid(score) && w.A.Get(score).Valid(k), w.A.Get(score).Get(k)
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}
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// set alignment traceback for wavefront=score, diag=k
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func (w *WavefrontComponent) SetTraceback(score int, k int, val traceback) {
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w.A.Get(score).Set(k, val)
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}
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// get hi for wavefront=score
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func (w *WavefrontComponent) GetLoHi(score int) (bool, int, int) {
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// if lo[score] and hi[score] are valid
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if w.lo.Valid(score) && w.hi.Valid(score) {
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// return lo[score] hi[score]
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return true, w.lo.Get(score), w.hi.Get(score)
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} else {
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return false, 0, 0
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}
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}
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// set hi for wavefront=score
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func (w *WavefrontComponent) SetLoHi(score int, lo int, hi int) {
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// lo[score] = lo
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w.lo.Set(score, lo)
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// hi[score] = hi
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w.hi.Set(score, hi)
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// preemptively setup w.A
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a := NewWavefront[traceback](lo, hi)
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w.A.Set(score, a)
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// preemptively setup w.W
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b := NewWavefront[int](lo, hi)
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w.W.Set(score, b)
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}
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